Continuity mistake: Throughout the film, Maj. Casey Schuler's hair is dyed strawberry blonde. In the scene where he convulses from being infected with the virus and is rushed to an available hospital bed, his hair color changes to his natural dark locks. In his death scene a few minutes later, his hair color is back to being strawberry blonde.
Factual error: In the scenes where Daniels and Salt are flying together in the helicopter, the pilot, Salt, would be in the right seat. Although it is possible to fly the helicopter from either seat, the primary controls are on the right of the helicopter (Loach, Hughes OH-6 included). Even an inexperienced pilot would never jump into the left seat when the other person has no flight experience. Left seat primary controls are in fixed wing aircraft.
Other mistake: About half an hour into the film, Schuler and Daniels go down to the level 4 bio-lab. They pass through a number of doors that earlier and later in the film reqire an ID card or hand-print scan to access, but they don't use either on any door. (A security guard seems to usher them through one door, but surely such a high security lab would require positive ID at each entry point).
Continuity mistake: The bomber approaching the town is military green in all scenes but one. One shot, however, is of a bright yellow plane. If that's just the sunlight, then note that a minute and a half later, the plane (which has supposedly been approaching from the same direction) now has sun shining on its right side rather than left.
Factual error: At the beginning of the movie, a military plane that appears to be a DC-3 drops a large bomb out from its tail area. Problem being, the DC-3 has no door under its tail, as is found on modern military transport planes or the one used at the end of the film. The DC-3 only has side doors.
Other mistake: Before getting on the plane, Col. Daniels has a conversation with General Ford. Ford salutes Daniels, which is incorrect; as the lower ranking officer, Daniels should have saluted first as a sign of respect and protocol.
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Factual error: When Sam Daniels and Casey are walking to the BSL-4 lab we see the shoulder insignia on Casey's coat are silver oak leaves. Silver oak leaves are the insignia of an O-5, Lieutenant Colonel, but Casey is supposed to be an O-4, Major (which would be represented by gold oak leaves). The only possible explanation is that Casey was promoted after the trip to Zaire, however this is extremely unlikely; if he were promoted to O-5 he would likely be given his own crew and no longer a member of Daniel's staff.
Audio problem: Between 1:12:26 and 1:12:37 into the film, as the chopper lands near the outer perimeter of the cordon for Cedar Creek, the audio has mixed into it civilian ATC conversations from a commercial airport, instead of military center. Specifically, ".cleared to land 24R.Delta 1781 cross runway 24L.". The chopper should not be on civilian freq at an airport far from his operating area or landing zone. You can compare the audio at 1:25:20 when the army loach leaves the flight line, ATC audio is presumed to be on the right freq and is ordered to RTB / land.